Mercurial > repos > galaxyp > openms_topperc
changeset 0:fc7bbbcd8194 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 13:01:11 -0500 |
| parents | |
| children | a6574e6fc144 |
| files | SKIP_TOOLS_FILE.txt TopPerc.xml datatypes_conf.xml filetypes.txt macros.xml readme.md repository_dependencies.xml test-data/DecoyDatabase_input.fasta test-data/DecoyDatabase_output.fasta tool.conf |
| diffstat | 10 files changed, 1052 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SKIP_TOOLS_FILE.txt Wed Mar 01 13:01:11 2017 -0500 @@ -0,0 +1,9 @@ +OMSSAAdapter +MyriMatchAdapter +PepNovoAdapter +SeedListGenerator +SpecLibSearcher +MapAlignerIdentification +MapAlignerPoseClustering +MapAlignerSpectrum +MapAlignerRTTransformer
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/TopPerc.xml Wed Mar 01 13:01:11 2017 -0500 @@ -0,0 +1,241 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> +<!--Proposed Tool Section: [Utilities]--> +<tool id="TopPerc" name="TopPerc" version="2.1.0"> + <description>Facilitate input to Percolator and reintegrate.</description> + <macros> + <token name="@EXECUTABLE@">TopPerc</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>TopPerc + +#if $param_percolator_executable: + -percolator_executable $param_percolator_executable +#end if +#if $param_in_target: + -in_target $param_in_target +#end if +#if $param_in_decoy: + -in_decoy $param_in_decoy +#end if +#if $param_out: + -out $param_out +#end if +#if $param_enzyme: + -enzyme "$param_enzyme" +#end if +#if $param_X: + -X $param_X +#end if +#if $param_e: + -e +#end if +#if $param_Z: + -Z +#end if +#if $param_p: + -p $param_p +#end if +#if $param_n: + -n $param_n +#end if +#if $param_F: + -F $param_F +#end if +#if $param_t: + -t $param_t +#end if +#if $param_i: + -i $param_i +#end if +#if $param_x: + -x +#end if +#if $param_f: + -f $param_f +#end if +#if $param_J: + -J $param_J +#end if +#if $param_k: + -k $param_k +#end if +#if $param_w: + -w $param_w +#end if +#if $param_W: + -W $param_W +#end if +#if $param_V: + -V "$param_V" +#end if +#if $param_v: + -v $param_v +#end if +#if $param_u: + -u +#end if +#if $param_R: + -R +#end if +#if $param_O: + -O +#end if +#if $param_S: + -S $param_S +#end if +#if $param_K: + -K +#end if +#if $param_D: + -D +#end if +#if $param_B: + -B $param_B +#end if +#if $param_U: + -U +#end if +#if $param_s: + -s +#end if +#if $param_A: + -A +#end if +#if $param_a: + -a $param_a +#end if +#if $param_b: + -b $param_b +#end if +#if $param_G: + -G $param_G +#end if +#if $param_g: + -g +#end if +#if $param_I: + -I +#end if +#if $param_q: + -q +#end if +#if $param_N: + -N +#end if +#if $param_E: + -E +#end if +#if $param_C: + -C +#end if +#if $param_d: + -d $param_d +#end if +#if $param_P: + -P "$param_P" +#end if +#if $param_T: + -T +#end if +#if $param_Y: + -Y +#end if +#if $param_H: + -H +#end if +#if $param_fido_truncation: + -fido-truncation +#end if +#if $param_Q: + -Q +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_force: + -force +#end if +#end if +</command> + <inputs> + <param name="param_percolator_executable" type="data" format="text" label="Path to the percolator binary" help="(-percolator_executable) "/> + <param name="param_in_target" type="data" format="mzid" optional="False" label="Input target file" help="(-in_target) "/> + <param name="param_in_decoy" type="data" format="mzid" optional="False" label="Input decoy file" help="(-in_decoy) "/> + <param name="param_enzyme" type="text" size="30" value="trypsin" label="Type of enzyme: no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin" help="(-enzyme) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_e" display="radio" type="boolean" truevalue="-e" falsevalue="" checked="false" optional="True" label="read xml-input format (pin) from standard input" help="(-e) "/> + <param name="param_Z" display="radio" type="boolean" truevalue="-Z" falsevalue="" checked="false" optional="True" label="Include decoys (PSMs, peptides and/or proteins) in the xml-output" help="(-Z) Only available if -X is used"/> + <param name="param_p" type="float" value="0.0" label="Cpos, penalty for mistakes made on positive examples" help="(-p) Set by cross validation if not specified"/> + <param name="param_n" type="float" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="(-n) Set by cross validation if not specified"/> + <param name="param_F" type="float" value="0.01" label="False discovery rate threshold to define positive examples in training" help="(-F) Set by cross validation if 0. Default is 0.01"/> + <param name="param_t" type="float" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help="(-t) Default is 0.01"/> + <param name="param_i" type="integer" value="0" label="Maximal number of iterations" help="(-i) "/> + <param name="param_x" display="radio" type="boolean" truevalue="-x" falsevalue="" checked="false" optional="True" label="Quicker execution by reduced internal cross-validation" help="(-x) "/> + <param name="param_f" type="float" value="0.6" label="Fraction of the negative data set to be used as train set when only providing one negative set, remaining examples will be used as test set" help="(-f) Set to 0.6 by default"/> + <param name="param_k" type="data" format="text" label="Input file given in the deprecated pin-xml format generated by" help="(-k) e.g. sqt2pin with the -k option"/> + <param name="param_W" type="data" format="text" label="Read initial weights to the given file" help="(-W) "/> + <param name="param_V" type="text" size="30" label="The most informative feature given as the feature name, can be negated to indicate that a lower value is bette" help="(-V) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_v" type="integer" value="2" label="Set verbosity of output: 0=no processing info, 5=all, default is 2" help="(-v) "/> + <param name="param_u" display="radio" type="boolean" truevalue="-u" falsevalue="" checked="false" optional="True" label="Use unit normalization [0-1] instead of standard deviation normalization" help="(-u) "/> + <param name="param_R" display="radio" type="boolean" truevalue="-R" falsevalue="" checked="false" optional="True" label="Measure performance on test set each iteration" help="(-R) "/> + <param name="param_O" display="radio" type="boolean" truevalue="-O" falsevalue="" checked="false" optional="True" label="Override error check and do not fall back on default score vector in case of suspect score vecto" help="(-O) "/> + <param name="param_S" type="integer" value="1" label="Setting seed of the random number generato" help="(-S) Default value is 1"/> + <param name="param_K" display="radio" type="boolean" truevalue="-K" falsevalue="" checked="false" optional="True" label="Retention time features calculated as in Klammer et al" help="(-K) "/> + <param name="param_D" display="radio" type="boolean" truevalue="-D" falsevalue="" checked="false" optional="True" label="Include description of correct features" help="(-D) "/> + <param name="param_U" display="radio" type="boolean" truevalue="-U" falsevalue="" checked="false" optional="True" label="Do not remove redundant peptides, keep all PSMS and exclude peptide level probabilities" help="(-U) "/> + <param name="param_s" display="radio" type="boolean" truevalue="-s" falsevalue="" checked="false" optional="True" label="skip validation of input file against xml schema" help="(-s) "/> + <param name="param_A" display="radio" type="boolean" truevalue="-A" falsevalue="" checked="false" optional="True" label="output protein level probabilities" help="(-A) "/> + <param name="param_a" type="float" value="0.0" label="Probability with which a present protein emits an associated peptide (to be used jointly with the -A option)" help="(-a) Set by grid search if not specified"/> + <param name="param_b" type="float" value="0.0" label="Probability of the creation of a peptide from noise (to be used jointly with the -A option)" help="(-b) Set by grid search if not specified"/> + <param name="param_G" type="float" value="0.0" label="Prior probability of that a protein is present in the sample ( to be used with the -A option)" help="(-G) Set by grid search if not specified"/> + <param name="param_g" display="radio" type="boolean" truevalue="-g" falsevalue="" checked="false" optional="True" label="treat ties as if it were one protein (Only valid if option -A is active)" help="(-g) "/> + <param name="param_I" display="radio" type="boolean" truevalue="-I" falsevalue="" checked="false" optional="True" label="use pi_0 value when calculating empirical q-values (no effect if option Q is activated) (Only valid if option -A is active)" help="(-I) "/> + <param name="param_q" display="radio" type="boolean" truevalue="-q" falsevalue="" checked="false" optional="True" label="output empirical q-values and p-values (from target-decoy analysis) (Only valid if option -A is active)" help="(-q) "/> + <param name="param_N" display="radio" type="boolean" truevalue="-N" falsevalue="" checked="false" optional="True" label="disactivates the grouping of proteins with similar connectivity, for example if proteins P1 and P2 have the same peptides matching both of them, P1 and P2 will not be grouped as one protein (Only valid if option -A is active)" help="(-N) "/> + <param name="param_E" display="radio" type="boolean" truevalue="-E" falsevalue="" checked="false" optional="True" label="Proteins graph will not be separated in sub-graphs (Only valid if option -A is active)" help="(-E) "/> + <param name="param_C" display="radio" type="boolean" truevalue="-C" falsevalue="" checked="false" optional="True" label="it does not prune peptides with a very low score (~0.0) which means that if a peptide with a very low score is matching two proteins, when we prune the peptide,it will be duplicated to generate two new protein groups (Only valid if option -A is active)" help="(-C) "/> + <param name="param_d" type="integer" value="0" label="Setting depth 0 or 1 or 2 from low depth to high depth(less computational time) of the grid search for the estimation Alpha,Beta and Gamma parameters for fido(Only valid if option -A is active)" help="(-d) Default value is 0"/> + <param name="param_P" type="text" size="30" value="random" label="Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (by default : random) (Only valid if option -A is active)" help="(-P) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_T" display="radio" type="boolean" truevalue="-T" falsevalue="" checked="false" optional="True" label="Reduce the tree of proteins (removing low scored proteins) in order to estimate alpha,beta and gamma faster.(Only valid if option -A is active)" help="(-T) "/> + <param name="param_Y" display="radio" type="boolean" truevalue="-Y" falsevalue="" checked="false" optional="True" label="Use target decoy competition to compute peptide probabilities.(recommended when using -A)" help="(-Y) "/> + <param name="param_H" display="radio" type="boolean" truevalue="-H" falsevalue="" checked="false" optional="True" label="Q-value threshold that will be used in the computation of the MSE and ROC AUC score in the grid search (recommended 0.05 for normal size datasets and 0.1 for big size datasets).(Only valid if option -A is active)" help="(-H) "/> + <param name="param_fido_truncation" display="radio" type="boolean" truevalue="-fido-truncation" falsevalue="" checked="false" optional="True" label="Proteins with a very low score (< 0.001) will be truncated (assigned 0.0 probability).(Only valid if option -A is active)" help="(-fido-truncation) "/> + <param name="param_Q" display="radio" type="boolean" truevalue="-Q" falsevalue="" checked="false" optional="True" label="Uses protein group level inference, each cluster of proteins is either present or not, therefore when grouping proteins discard all possible combinations for each group.(Only valid if option -A is active and -N is inactive)" help="(-Q) "/> + <expand macro="advanced_options"> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" format="data"/> + <data name="param_X" format="data"/> + <data name="param_J" format="data"/> + <data name="param_w" format="data"/> + <data name="param_B" format="data"/> + </outputs> + <help>Facilitate input to Percolator and reintegrate. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_TopPerc.html</help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Wed Mar 01 13:01:11 2017 -0500 @@ -0,0 +1,33 @@ +<?xml version='1.0' encoding='UTF-8'?> +<datatypes> + <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> + <datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml"/> + <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/> + <datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXM" mimetype="application/xml"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text"/> + <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/> + <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf"/> + <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml"/> + <datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/> + <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml"/> + <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp"/> + <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/> + <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular"/> + <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml"/> + <datatype extension="xml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/> + <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml"/> + <datatype extension="grid" type="galaxy.datatypes.data:Grid"/> + <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml"/> + <datatype extension="png" type="galaxy.datatypes.images:Png" mimetype="image/png"/> + <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml"/> + <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml"/> + <datatype extension="html" type="galaxy.datatypes.text:Html" mimetype="text/html"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text"/> + <datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text"/> + </registration> +</datatypes>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filetypes.txt Wed Mar 01 13:01:11 2017 -0500 @@ -0,0 +1,29 @@ +# CTD type # Galaxy type # Long Galaxy data type # Mimetype +csv tabular galaxy.datatypes.tabular:Tabular +fasta fasta galaxy.datatypes.sequence:Fasta +FASTA fasta galaxy.datatypes.sequence:Fasta +ini txt galaxy.datatypes.data:Text +txt txt galaxy.datatypes.data:Text +options txt galaxy.datatypes.data:Text +grid grid galaxy.datatypes.data:Grid +html html galaxy.datatypes.text:Html text/html +HTML html galaxy.datatypes.text:Html text/html +TraML traml galaxy.datatypes.proteomics:TraML application/xml +traML traml galaxy.datatypes.proteomics:TraML application/xml +XML xml galaxy.datatypes.xml:GenericXml application/xml +consensusXML consensusxml galaxy.datatypes.proteomics:ConsensusXML application/xml +edta tabular galaxy.datatypes.tabular:Tabular +featureXML featurexml galaxy.datatypes.proteomics:FeatureXML application/xml +idXML idxml galaxy.datatypes.proteomics:IdXM application/xml +mzML mzml galaxy.datatypes.proteomics:MzML application/xml +mzXML mzxml galaxy.datatypes.proteomics:MzXML application/xml +pepXML pepxml galaxy.datatypes.proteomics:PepXml application/xml +qcML qcml galaxy.datatypes.xml:GenericXml application/xml +trafoXML trafoxml galaxy.datatypes.xml:GenericXml application/xml +tsv tabular galaxy.datatypes.tabular:Tabular +xsd txt galaxy.datatypes.data:Text +mzq mzq galaxy.datatypes.proteomics:MzQuantML application/xml +msp msp galaxy.datatypes.proteomics:Msp +mzid mzid galaxy.datatypes.proteomics:MzIdentML application/xml +png png galaxy.datatypes.images:Png image/png +mgf mgf galaxy.datatypes.proteomics:Mgf \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Mar 01 13:01:11 2017 -0500 @@ -0,0 +1,35 @@ +<?xml version='1.0' encoding='UTF-8'?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.1">openms</requirement> + <requirement type="package" version="15.12.15.2">xtandem</requirement> + <requirement type="package" version="1.0">fido</requirement> + <requirement type="package" version="2016.10.26">msgf_plus</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <regex match="Exception:"/> + </stdio> + </xml> + <xml name="references"> + <citations> + <citation type="doi">doi:10.1186/1471-2105-9-163</citation> + </citations> + </xml> + <xml name="advanced_options"> + <conditional name="adv_opts"> + <param name="adv_opts_selector" type="select" label="Advanced Options"> + <option value="basic" selected="True">Hide Advanced Options</option> + <option value="advanced">Show Advanced Options</option> + </param> + <when value="basic"/> + <when value="advanced"> + <yield/> + </when> + </conditional> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.md Wed Mar 01 13:01:11 2017 -0500 @@ -0,0 +1,165 @@ +Galaxy wrapper for OpenMS +========================= + +OpenMS is an open-source software C++ library for LC/MS data management and analyses. +It offers an infrastructure for the rapid development of mass spectrometry related software. +OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux. + +More informations are available at: + + * https://github.com/OpenMS/OpenMS + * http://open-ms.sourceforge.net + + +Generating OpenMS wrappers +========================== + + * install OpenMS (you can do this automatically through the Tool Shed) + * create a folder called CTD + * inside of your new installed openms/bin folder, execute the following command: + + ```bash + for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; + ``` + + * `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). + + * clone or install CTDopts + + ```bash + git clone https://github.com/genericworkflownodes/CTDopts + ``` + + * add CTDopts to your `$PYTHONPATH` + + ```bash + export PYTHONPATH=/home/user/CTDopts/ + ``` + + * clone or install CTD2Galaxy + + ```bash + git clone https://github.com/blankclemens/CTD2Galaxy.git + ``` + + * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. + + ```bash + python generator.py \ + -i /PATH/TO/YOUR/CTD/*.ctd \ + -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ + -d datatypes_conf.xml -g openms \ + -b version log debug test no_progress threads \ + in_type executable myrimatch_executable \ + fido_executable fidocp_executable \ + omssa_executable pepnovo_executable \ + xtandem_executable param_model_directory \ + java_executable java_memory java_permgen \ + -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ + -s PATH/TO/SKIP_TOOLS_FILES.txt + ``` + + + * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: + + ``` + sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml + sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml + sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml + sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml + sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml + ``` + + * For some tools, additional work has to be done. In `MSGFPlusAdapter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): + + ``` + <command><![CDATA[ + + ## check input file type + #set $in_type = $param_in.ext + + ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files + ln -s '$param_in' 'param_in.${in_type}' && + ln -s '$param_database' param_database.fasta && + ## find location of the MSGFPlus.jar file of the msgf_plus conda package + MSGF_JAR=\$(msgf_plus -get_jar_path) && + + MSGFPlusAdapter + -executable \$MSGF_JAR + #if $param_in: + -in 'param_in.${in_type}' + #end if + #if $param_out: + -out $param_out + #end if + #if $param_mzid_out: + -mzid_out $param_mzid_out + #end if + #if $param_database: + -database param_database.fasta + #end if + + [...] + ]]> + ``` + * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line + + -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit + + and change it to + + -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit" + + * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: + + <data name="param_out" metadata_source="param_in" auto_format="true"/> + + * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. + + ``` + <tests> + <test> + <param name="param_in" value="DecoyDatabase_input.fasta"/> + <output name="param_out" file="DecoyDatabase_output.fasta"/> + </test> + </tests> + ``` + + + * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable and are therefore in `SKIP_TOOLS_FILES.txt`: + * SeedListGenerator + * SpecLibSearcher + * MapAlignerIdentification + * MapAlignerPoseClustering + * MapAlignerSpectrum + * MapAlignerRTTransformer + + * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well: + * OMSSAAdapter + * MyrimatchAdapter + + * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed: + * PepNovoAdapter + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Wed Mar 01 13:01:11 2017 -0500 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Required proteomics dependencies."> + <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DecoyDatabase_input.fasta Wed Mar 01 13:01:11 2017 -0500 @@ -0,0 +1,146 @@ +>12 +MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI +STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL +YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM +VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR +DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL +MIIVPTDTQNIFFMSKVTNPKQA +>18 +MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMK +QLNIIQNAEAVHFFCNYEESRGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQ +NASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLITMACGSCSNENALKTIFMWYR +SKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS +FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGG +DNHASDDFFRKLRDIARKHGCAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMM +TGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIKREDLLNNAAHAGKALLTGLL +DLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF +RDHHAHLFLNIFSDILADFK +>88 +MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIE +NIEEDFRNGLKLMLLLEVISGERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAE +EIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLWCQRKTAPYRNVNIQNFHTSW +KDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP +DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRT +IPWLENRTPEKTMQAMQKKLEDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAF +MPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLEHLAEKFRQKASTHETWAYGK +EQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN +DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQ +DMFIVHSIEEIQSLITAHEQFKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYS +TVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRRQFAAQANAIGPWIQNKMEEI +ARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI +RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRA +CLISMGYDLGEAEFARIMTLVDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILAS +DKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALDYAAFSSALYGESDL +>112 +MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGP +PRCPWQDDAFIRRGGPGKGKELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWR +RLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLVLLTAVLLAFHAAPARPQPAY +VALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW +CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTN +VIGICTHYPAEVSQRQAFQETRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINT +KKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQELVMTLNELFARFDKLAAENHC +LRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV +HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNA +YLKEQHIETFLILGASQKRKEEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFR +QMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQLRKDHVRRFLLTFQREDLEKK +YSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC +GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLT +PADITACHLQQLNYSLGLDAPLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLA +MIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNETFDGLDCPAAGRVALKYMTPV +ILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF +LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIIS +EERFRQLEKIKTIGSTYMAASGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNN +FQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDSTGVPDRIQVTTDLYQVLAAKG +YQLECRGVVKVKGKGEMTTYFLNGGPSS +>114 +MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGS +GSGGSGKASDPAGGGPNHHAPQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASG +SGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNSFKSRDLERLYQRYFLGQRRK +SEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT +YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTS +LLQVILQVVIPRLAVISINQVVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEAR +LRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQHQFHRIYIHRYENVSILFADV +KGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH +CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKL +ESGGIPGRIHISKATLDCLNGDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPED +IVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLAALTRNSINLLPNHLAQALHV +QSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF +IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINE +TYLARNVIIFASILINFLGAILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTG +VLAMVTCAVFLRLNSVLKLAVLLIMIAIYALLTETVYAGLFLRYDNLNHSGEDFLGTKEV +SLLLMAMFLLAVFYHGQQLEYTARLDFLWRVQAKEEINEMKELREHNENMLRNILPSHVA +RHFLEKDRDNEELYSQSYDAVGVMFASIPGFADFYSQTEMNNQGVECLRLLNEIIADFDE +LLGEDRFQDIEKIKTIGSTYMAVSGLSPEKQQCEDKWGHLCALADFSLALTESIQEINKH +SFNNFELRIGISHGSVVAGVIGAKKPQYDIWGKTVNLASRMDSTGVSGRIQVPEETYLIL +KDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV +QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP +>143 +MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQ +LNSIQKNHVHIANPDFIWKSIREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCP +DSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKVGMEGGQEAVVVELQCSRDSR +DCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQL +ASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGI +LLLVKAALKNGETAEQLQKMMTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVC +ETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVLQNHHSKSPVDVLQIFRVGRV +NETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSD +SLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVT +TDFEDDEFVVYKTNQVKMKYIIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQL +PDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVIVFQTYTNKSHVPIEAKYIFP +LDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGN +LPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTK +QSFSLTMSIEMPYVIEFIFSDTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYL +PRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIICLDCSSSMEGVTFLQAKQIAL +HALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYL +SLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCG +AGVFEYFNAKSKHSWRKQIEDQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFL +NDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTTGTMIHKLAARALIRDYEDGI +LHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAK +EDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSED +FEEDGLGVLPAFTSNLERGGVEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILA +PAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFDASQFSQGPVPGTCADWIPQS +ASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFS +LPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCL +LEESVGSLEGSRCPVFAFQSSDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDE +IVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNTNGLHSFLKQKGIQSLGVKGR +ECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTE +GQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG +>213 +MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPF +EDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEP +ERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLF +FAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV +ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLK +ECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYAR +RHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFE +QLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV +LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTL +SEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLV +AASQAALGL +>230 +MPHSYPALSAEQKKELSDIALRIVAPGKGILAADESVGSMAKRLSQIGVENTEENRRLYR +QVLFSADDRVKKCIGGVIFFHETLYQKDDNGVPFVRTIQDKGIVVGIKVDKGVVPLAGTD +GETTTQGLDGLSERCAQYKKDGADFAKWRCVLKISERTPSALAILENANVLARYASICQQ +NGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHAC +PIKYTPEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEASFNLNAINRCPLPRPWALTF +SYGRALQASALNAWRGQRDNAGAATEEFIKRAEVNGLAAQGKYEGSGEDGGAAAQSLYIA +NHAY +>231 +MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQ +EKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGK +EFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKP +AVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAK +HNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCA +LLSCTSHKDYPFHEEF +>242 +MATYKVRVATGTDLLSGTRDSISLTIVGTQGESHKQLLNHFGRDFATGAVGQYTVQCPQD +LGELIIIRLHKERYAFFPKDPWYCNYVQICAPNGRIYHFPAYQWMDGYETLALREATGKT +TADDSLPVLLEHRKEEIRAKQDFYHWRVFLPGLPSYVHIPSYRPPVRRHRNPNRPEWNGY +IPGFPILINFKATKFLNLNLRYSFLKTASFFVRLGPMALAFKVRGLLDCKHSWKRLKDIR +KIFPGKKSVVSEYVAEHWAEDTFFGYQYLNGVNPGLIRRCTRIPDKFPVTDDMVAPFLGE +GTCLQAELEKGNIYLADYRIMEGIPTVELSGRKQHHCAPLCLLHFGPEGKMMPIAIQLSQ +TPGPDCPIFLPSDSEWDWLLAKTWVRYAEFYSHEAIAHLLETHLIAEAFCLALLRNLPMC +HPLYKLLIPHTRYTVQINSIGRAVLLNEGGLSAKGMSLGVEGFAGVMVRALSELTYDSLY +LPNDFVERGVQDLPGYYYRDDSLAVWNALEKYVTEIITYYYPSDAAVEGDPELQSWVQEI +FKECLLGRESSGFPRCLRTVPELIRYVTIVIYTCSAKHAAVNTGQMEFTAWMPNFPASMR +NPPIQTKGLTTLETFMDTLPDVKTTCITLLVLWTLSREPDDRRPLGHFPDIHFVEEAPRR +SIEAFRQRLNQISHDIRQRNKCLPIPYYYLDPVLIENSISI
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DecoyDatabase_output.fasta Wed Mar 01 13:01:11 2017 -0500 @@ -0,0 +1,228 @@ +>12 +MERMLPLLALGLLAAGFCPAVLCHPNSPLDEENLTQENQDRGTHVDLGLASANVDFAFSLYKQLVLKAPDKNVIFSPLSI +STALAFLSLGAHNTTLTEILKGLKFNLTETSEAEIHQSFQHLLRTLNQSSDELQLSMGNAMFVKEQLSLLDRFTEDAKRL +YGSEAFATDFQDSAAAKKLINDYVKNGTRGKITDLIKDLDSQTMMVLVNYIFFKAKWEMPFDPQDTHQSRFYLSKKKWVM +VPMMSLHHLTIPYFRDEELSCTVVELKYTGNASALFILPDQDKMEEVEAMLLPETLKRWRDSLEFREIGELYLPKFSISR +DYNLNDILLQLGIEEAFTSKADLSGITGARNLAVSQVVHKAVLDVFEEGTEASAATAVKITLLSALVETRTIVRFNRPFL +MIIVPTDTQNIFFMSKVTNPKQA +>18 +MASMLLAQRLACSFQHSYRLLVPGSRHISQAAAKVDVEFDYDGPLMKTEVPGPRSQELMKQLNIIQNAEAVHFFCNYEES +RGNYLVDVDGNRMLDLYSQISSVPIGYSHPALLKLIQQPQNASMFVNRPALGILPPENFVEKLRQSLLSVAPKGMSQLIT +MACGSCSNENALKTIFMWYRSKERGQRGFSQEELETCMINQAPGCPDYSILSFMGAFHGRTMGCLATTHSKAIHKIDIPS +FDWPIAPFPRLKYPLEEFVKENQQEEARCLEEVEDLIVKYRKKKKTVAGIIVEPIQSEGGDNHASDDFFRKLRDIARKHG +CAFLVDEVQTGGGCTGKFWAHEHWGLDDPADVMTFSKKMMTGGFFHKEEFRPNAPYRIFNTWLGDPSKNLLLAEVINIIK +REDLLNNAAHAGKALLTGLLDLQARYPQFISRVRGRGTFCSFDTPDDSIRNKLILIARNKGVVLGGCGDKSIRFRPTLVF +RDHHAHLFLNIFSDILADFK +>88 +MNQIEPGVQYNYVYDEDEYMIQEEEWDRDLLLDPAWEKQQRKTFTAWCNSHLRKAGTQIENIEEDFRNGLKLMLLLEVIS +GERLPKPDRGKMRFHKIANVNKALDYIASKGVKLVSIGAEEIVDGNVKMTLGMIWTIILRFAIQDISVEETSAKEGLLLW +CQRKTAPYRNVNIQNFHTSWKDGLGLCALIHRHRPDLIDYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKP +DERAIMTYVSCFYHAFAGAEQAETAANRICKVLAVNQENERLMEEYERLASELLEWIRRTIPWLENRTPEKTMQAMQKKL +EDFRDYRRKHKPPKVQEKCQLEINFNTLQTKLRISNRPAFMPSEGKMVSDIAGAWQRLEQAEKGYEEWLLNEIRRLERLE +HLAEKFRQKASTHETWAYGKEQILLQKDYESASLTEVRALLRKHEAFESDLAAHQDRVEQIAAIAQELNELDYHDAVNVN +DRCQKICDQWDRLGTLTQKRREALERMEKLLETIDQLHLEFAKRAAPFNNWMEGAMEDLQDMFIVHSIEEIQSLITAHEQ +FKATLPEADGERQSIMAIQNEVEKVIQSYNIRISSSNPYSTVTMDELRTKWDKVKQLVPIRDQSLQEELARQHANERLRR +QFAAQANAIGPWIQNKMEEIARSSIQITGALEDQMNQLKQYEHNIINYKNNIDKLEGDHQLIQEALVFDNKHTNYTMEHI +RVGWELLLTTIARTINEVETQILTRDAKGITQEQMNEFRASFNHFDRRKNGLMDHEDFRACLISMGYDLGEAEFARIMTL +VDPNGQGTVTFQSFIDFMTRETADTDTAEQVIASFRILASDKPYILAEELRRELPPDQAQYCIKRMPAYSGPGSVPGALD +YAAFSSALYGESDL +>112 +MSWFSGLLVPKVDERKTAWGERNGQKRSRRRGTRAGGFCTPRYMSCLRDAEPPSPTPAGPPRCPWQDDAFIRRGGPGKGK +ELGLRAVALGFEDTEVTTTAGGTAEVAPDAVPRSGRSCWRRLVQVFQSKQFRSAKLERLYQRYFFQMNQSSLTLLMAVLV +LLTAVLLAFHAAPARPQPAYVALLACAAALFVGLMVVCNRHSFRQDSMWVVSYVVLGILAAVQVGGALAADPRSPSAGLW +CPVFFVYIAYTLLPIRMRAAVLSGLGLSTLHLILAWQLNRGDAFLWKQLGANVLLFLCTNVIGICTHYPAEVSQRQAFQE +TRGYIQARLHLQHENRQQERLLLSVLPQHVAMEMKEDINTKKEDMMFHKIYIQKHDNVSILFADIEGFTSLASQCTAQEL +VMTLNELFARFDKLAAENHCLRIKILGDCYYCVSGLPEARADHAHCCVEMGVDMIEAISLVREVTGVNVNMRVGIHSGRV +HCGVLGLRKWQFDVWSNDVTLANHMEAGGRAGRIHITRATLQYLNGDYEVEPGRGGERNAYLKEQHIETFLILGASQKRK +EEKAMLAKLQRTRANSMEGLMPRWVPDRAFSRTKDSKAFRQMGIDDSSKDNRGTQDALNPEDEVDEFLSRAIDARSIDQL +RKDHVRRFLLTFQREDLEKKYSRKVDPRFGAYVACALLVFCFICFIQLLIFPHSTLMLGIYASIFLLLLITVLICAVYSC +GSLFPKALQRLSRSIVRSRAHSTAVGIFSVLLVFTSAIANMFTCNHTPIRSCAARMLNLTPADITACHLQQLNYSLGLDA +PLCEGTMPTCSFPEYFIGNMLLSLLASSVFLHISSIGKLAMIFVLGLIYLVLLLLGPPATIFDNYDLLLGVHGLASSNET +FDGLDCPAAGRVALKYMTPVILLVFALALYLHAQQVESTARLDFLWKLQATGEKEEMEELQAYNRRLLHNILPKDVAAHF +LARERRNDELYYQSCECVAVMFASIANFSEFYVELEANNEGVECLRLLNEIIADFDEIISEERFRQLEKIKTIGSTYMAA +SGLNASTYDQVGRSHITALADYAMRLMEQMKHINEHSFNNFQMKIGLNMGPVVAGVIGARKPQYDIWGNTVNVSSRMDST +GVPDRIQVTTDLYQVLAAKGYQLECRGVVKVKGKGEMTTYFLNGGPSS +>114 +MELSDVRCLTGSEELYTIHPTPPAGDGRSASRPQRLLWQTAVRHITEQRFIHGHRGGSGSGSGGSGKASDPAGGGPNHHA +PQLSGDSALPLYSLGPGERAHSTCGTKVFPERSGSGSASGSGGGGDLGFLHLDCAPSNSDFFLNGGYSYRGVIFPTLRNS +FKSRDLERLYQRYFLGQRRKSEVVMNVLDVLTKLTLLVLHLSLASAPMDPLKGILLGFFTGIEVVICALVVVRKDTTSHT +YLQYSGVVTWVAMTTQILAAGLGYGLLGDGIGYVLFTLFATYSMLPLPLTWAILAGLGTSLLQVILQVVIPRLAVISINQ +VVAQAVLFMCMNTAGIFISYLSDRAQRQAFLETRRCVEARLRLETENQRQERLVLSVLPRFVVLEMINDMTNVEDEHLQH +QFHRIYIHRYENVSILFADVKGFTNLSTTLSAQELVRMLNELFARFDRLAHEHHCLRIKILGDCYYCVSGLPEPRQDHAH +CCVEMGLSMIKTIRYVRSRTKHDVDMRIGIHSGSVLCGVLGLRKWQFDVWSWDVDIANKLESGGIPGRIHISKATLDCLN +GDYNVEEGHGKERNEFLRKHNIETYLIKQPEDSLLSLPEDIVKESVSSSDRRNSGATFTEGSWSPELPFDNIVGKQNTLA +ALTRNSINLLPNHLAQALHVQSGPEEINKRIEHTIDLRSGDKLRREHIKPFSLMFKDSSLEHKYSQMRDEVFKSNLVCAF +IVLLFITAIQSLLPSSRVMPMTIQFSILIMLHSALVLITTAEDYKCLPLILRKTCCWINETYLARNVIIFASILINFLGA +ILNILWCDFDKSIPLKNLTFNSSAVFTDICSYPEYFVFTGVLAMVTCAVFLRLNSVLKLAVLLIMIAIYALLTETVYAGL +FLRYDNLNHSGEDFLGTKEVSLLLMAMFLLAVFYHGQQLEYTARLDFLWRVQAKEEINEMKELREHNENMLRNILPSHVA +RHFLEKDRDNEELYSQSYDAVGVMFASIPGFADFYSQTEMNNQGVECLRLLNEIIADFDELLGEDRFQDIEKIKTIGSTY +MAVSGLSPEKQQCEDKWGHLCALADFSLALTESIQEINKHSFNNFELRIGISHGSVVAGVIGAKKPQYDIWGKTVNLASR +MDSTGVSGRIQVPEETYLILKDQGFAFDYRGEIYVKGISEQEGKIKTYFLLGRVQPNPFILPPRRLPGQYSLAAVVLGLV +QSLNRQRQKQLLNENNNTGIIKGHYNRRTLLSPSGTEPGAQAEGTDKSDLP +>143 +MVMGIFANCIFCLKVKYLPQQQKKKLQTDIKENGGKFSFSLNPQCTHIILDNADVLSQYQLNSIQKNHVHIANPDFIWKS +IREKRLLDVKNYDPYKPLDITPPPDQKASSSEVKTEGLCPDSATEEEDTVELTEFGMQNVEIPHLPQDFEVAKYNTLEKV +GMEGGQEAVVVELQCSRDSRDCPFLISSHFLLDDGMETRRQFAIKKTSEDASEYFENYIEELKKQGFLLREHFTPEATQL +ASEQLQALLLEEVMNSSTLSQEVSDLVEMIWAEALGHLEHMLLKPVNRISLNDVSKAEGILLLVKAALKNGETAEQLQKM +MTEFYRLIPHKGTMPKEVNLGLLAKKADLCQLIRDMVNVCETNLSKPNPPSLAKYRALRCKIEHVEQNTEEFLRVRKEVL +QNHHSKSPVDVLQIFRVGRVNETTEFLSKLGNVRPLLHGSPVQNIVGILCRGLLLPKVVEDRGVQRTDVGNLGSGIYFSD +SLSTSIKYSHPGETDGTRLLLICDVALGKCMDLHEKDFSLTEAPPGYDSVHGVSQTASVTTDFEDDEFVVYKTNQVKMKY +IIKFSMPGDQIKDFHPSDHTELEEYRPEFSNFSKVEDYQLPDAKTSSSTKAGLQDASGNLVPLEDVHIKGRIIDTVAQVI +VFQTYTNKSHVPIEAKYIFPLDDKAAVCGFEAFINGKHIVGEIKEKEEAQQEYLEAVTQGHGAYLMSQDAPDVFTVSVGN +LPPKAKVLIKITYITELSILGTVGVFFMPATVAPWQQDKALNENLQDTVEKICIKEIGTKQSFSLTMSIEMPYVIEFIFS +DTHELKQKRTDCKAVISTMEGSSLDSSGFSLHIGLSAAYLPRMWVEKHPEKESEACMLVFQPDLDVDLPDLASESEVIIC +LDCSSSMEGVTFLQAKQIALHALSLVGEKQKVNIIQFGTGYKELFSYPKHITSNTMAAEFIMSATPTMGNTDFWKTLRYL +SLLYPARGSRNILLVSDGHLQDESLTLQLVKRSRPHTRLFACGIGSTANRHVLRILSQCGAGVFEYFNAKSKHSWRKQIE +DQMTRLCSPSCHSVSVKWQQLNPDVPEALQAPAQVPSLFLNDRLLVYGFIPHCTQATLCALIQEKEFRTMVSTTELQKTT +GTMIHKLAARALIRDYEDGILHENETSHEMKKQTLKSLIIKLSKENSLITQFTSFVAVEKRDENESPFPDIPKVSELIAK +EDVDFLPYMSWQGEPQEAVRNQSLLASSEWPELRLSKRKHRKIPFSKRKMELSQPEVSEDFEEDGLGVLPAFTSNLERGG +VEKLLDLSWTESCKPTATEPLFKKVSPWETSTSSFFPILAPAVGSYLPPTARAHSPASLSFASYRQVASFGSAAPPRQFD +ASQFSQGPVPGTCADWIPQSASCPTGPPQNPPSSPYCGIVFSGSSLSSAQSAPLQHPGGFTTRPSAGTFPELDSPQLHFS +LPTDPDPIRGFGSYHPSASSPFHFQPSAASLTANLRLPMASALPEALCSQSRTTPVDLCLLEESVGSLEGSRCPVFAFQS +SDTESDELSEVLQDSCFLQIKCDTKDDSILCFLEVKEEDEIVCIQHWQDAVPWTELLSLQTEDGFWKLTPELGLILNLNT +NGLHSFLKQKGIQSLGVKGRECLLDLIATMLVLQFIRTRLEKEGIVFKSLMKMDDASISRNIPWAFEAIKQASEWVRRTE +GQYPSICPRLELGNDWDSATKQLLGLQPISTVSPLHRVLHYSQG +>213 +MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVAD +ESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLK +KYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAV +ARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVEND +EMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDE +FKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVV +LNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHK +PKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALGL +>230 +MPHSYPALSAEQKKELSDIALRIVAPGKGILAADESVGSMAKRLSQIGVENTEENRRLYRQVLFSADDRVKKCIGGVIFF +HETLYQKDDNGVPFVRTIQDKGIVVGIKVDKGVVPLAGTDGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKISERTPS +ALAILENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHVYLEGTLLKPNMVTPGHAC +PIKYTPEEIAMATVTALRRTVPPAVPGVTFLSGGQSEEEASFNLNAINRCPLPRPWALTFSYGRALQASALNAWRGQRDN +AGAATEEFIKRAEVNGLAAQGKYEGSGEDGGAAAQSLYIANHAY +>231 +MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLW +CTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGIS +NFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAK +HNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF +>242 +MATYKVRVATGTDLLSGTRDSISLTIVGTQGESHKQLLNHFGRDFATGAVGQYTVQCPQDLGELIIIRLHKERYAFFPKD +PWYCNYVQICAPNGRIYHFPAYQWMDGYETLALREATGKTTADDSLPVLLEHRKEEIRAKQDFYHWRVFLPGLPSYVHIP +SYRPPVRRHRNPNRPEWNGYIPGFPILINFKATKFLNLNLRYSFLKTASFFVRLGPMALAFKVRGLLDCKHSWKRLKDIR +KIFPGKKSVVSEYVAEHWAEDTFFGYQYLNGVNPGLIRRCTRIPDKFPVTDDMVAPFLGEGTCLQAELEKGNIYLADYRI +MEGIPTVELSGRKQHHCAPLCLLHFGPEGKMMPIAIQLSQTPGPDCPIFLPSDSEWDWLLAKTWVRYAEFYSHEAIAHLL +ETHLIAEAFCLALLRNLPMCHPLYKLLIPHTRYTVQINSIGRAVLLNEGGLSAKGMSLGVEGFAGVMVRALSELTYDSLY +LPNDFVERGVQDLPGYYYRDDSLAVWNALEKYVTEIITYYYPSDAAVEGDPELQSWVQEIFKECLLGRESSGFPRCLRTV +PELIRYVTIVIYTCSAKHAAVNTGQMEFTAWMPNFPASMRNPPIQTKGLTTLETFMDTLPDVKTTCITLLVLWTLSREPD +DRRPLGHFPDIHFVEEAPRRSIEAFRQRLNQISHDIRQRNKCLPIPYYYLDPVLIENSISI +>DECOY_12 +AQKPNTVKSMFFINQTDTPVIIMLFPRNFRVITRTEVLASLLTIKVATAASAETGEEFVDLVAKHVVQSVALNRAGTIGS +LDAKSTFAEEIGLQLLIDNLNYDRSISFKPLYLEGIERFELSDRWRKLTEPLLMAEVEEMKDQDPLIFLASANGTYKLEV +VTCSLEEDRFYPITLHHLSMMPVMVWKKKSLYFRSQHTDQPDFPMEWKAKFFIYNVLVMMTQSDLDKILDTIKGRTGNKV +YDNILKKAAASDQFDTAFAESGYLRKADETFRDLLSLQEKVFMANGMSLQLEDSSQNLTRLLHQFSQHIEAESTETLNFK +LGKLIETLTTNHAGLSLFALATSISLPSFIVNKDPAKLVLQKYLSFAFDVNASALGLDVHTGRDQNEQTLNEEDLPSNPH +CLVAPCFGAALLGLALLPLMREM +>DECOY_18 +KFDALIDSFINLFLHAHHDRFVLTPRFRISKDGCGGLVVGKNRAILILKNRISDDPTDFSCFTGRGRVRSIFQPYRAQLD +LLGTLLAKGAHAANNLLDERKIINIVEALLLNKSPDGLWTNFIRYPANPRFEEKHFFGGTMMKKSFTMVDAPDDLGWHEH +AWFKGTCGGGTQVEDVLFACGHKRAIDRLKRFFDDSAHNDGGESQIPEVIIGAVTKKKKRYKVILDEVEELCRAEEQQNE +KVFEELPYKLRPFPAIPWDFSPIDIKHIAKSHTTALCGMTRGHFAGMFSLISYDPCGPAQNIMCTELEEQSFGRQGREKS +RYWMFITKLANENSCSGCAMTILQSMGKPAVSLLSQRLKEVFNEPPLIGLAPRNVFMSANQPQQILKLLAPHSYGIPVSS +IQSYLDLMRNGDVDVLYNGRSEEYNCFFHVAEANQIINLQKMLEQSRPGPVETKMLPGDYDFEVDVKAAAQSIHRSGPVL +LRYSHQFSCALRQALLMSAM +>DECOY_88 +LDSEGYLASSFAAYDLAGPVSGPGSYAPMRKICYQAQDPPLERRLEEALIYPKDSALIRFSAIVQEATDTDATERTMFDI +FSQFTVTGQGNPDVLTMIRAFEAEGLDYGMSILCARFDEHDMLGNKRRDFHNFSARFENMQEQTIGKADRTLIQTEVENI +TRAITTLLLEWGVRIHEMTYNTHKNDFVLAEQILQHDGELKDINNKYNIINHEYQKLQNMQDELAGTIQISSRAIEEMKN +QIWPGIANAQAAFQRRLRENAHQRALEEQLSQDRIPVLQKVKDWKTRLEDMTVTSYPNSSSIRINYSQIVKEVENQIAMI +SQREGDAEPLTAKFQEHATILSQIEEISHVIFMDQLDEMAGEMWNNFPAARKAFELHLQDITELLKEMRELAERRKQTLT +GLRDWQDCIKQCRDNVNVADHYDLENLEQAIAAIQEVRDQHAALDSEFAEHKRLLARVETLSASEYDKQLLIQEKGYAWT +EHTSAKQRFKEALHELRELRRIENLLWEEYGKEAQELRQWAGAIDSVMKGESPMFAPRNSIRLKTQLTNFNIELQCKEQV +KPPKHKRRYDRFDELKKQMAQMTKEPTRNELWPITRRIWELLESALREYEEMLRENEQNVALVKCIRNAATEAQEAGAFA +HYFCSVYTMIAREDPKPTNVIDEADLMKPIDLHKEAIEMALNINGIPDDKNLKSYDILDPRHRHILACLGLGDKWSTHFN +QINVNRYPATKRQCWLLLGEKASTEEVSIDQIAFRLIITWIMGLTMKVNGDVIEEAGISVLKVGKSAIYDLAKNVNAIKH +FRMKGRDPKPLREGSIVELLLMLKLGNRFDEEINEIQTGAKRLHSNCWATFTKRQQKEWAPDLLLDRDWEEEQIMYEDED +YVYNYQVGPEIQNM +>DECOY_112 +SSPGGNLFYTTMEGKGKVKVVGRCELQYGKAALVQYLDTTVQIRDPVGTSDMRSSVNVTNGWIDYQPKRAGIVGAVVPGM +NLGIKMQFNNFSHENIHKMQEMLRMAYDALATIHSRGVQDYTSANLGSAAMYTSGITKIKELQRFREESIIEDFDAIIEN +LLRLCEVGENNAELEVYFESFNAISAFMVAVCECSQYYLEDNRRERALFHAAVDKPLINHLLRRNYAQLEEMEEKEGTAQ +LKWLFDLRATSEVQQAHLYLALAFVLLIVPTMYKLAVRGAAPCDLGDFTENSSALGHVGLLLDYNDFITAPPGLLLLVLY +ILGLVFIMALKGISSIHLFVSSALLSLLMNGIFYEPFSCTPMTGECLPADLGLSYNLQQLHCATIDAPTLNLMRAACSRI +PTHNCTFMNAIASTFVLLVSFIGVATSHARSRVISRSLRQLAKPFLSGCSYVACILVTILLLLFISAYIGLMLTSHPFIL +LQIFCIFCFVLLACAVYAGFRPDVKRSYKKELDERQFTLLFRRVHDKRLQDISRADIARSLFEDVEDEPNLADQTGRNDK +SSDDIGMQRFAKSDKTRSFARDPVWRPMLGEMSNARTRQLKALMAKEEKRKQSAGLILFTEIHQEKLYANREGGRGPEVE +YDGNLYQLTARTIHIRGARGGAEMHNALTVDNSWVDFQWKRLGLVGCHVRGSHIGVRMNVNVGTVERVLSIAEIMDVGME +VCCHAHDARAEPLGSVCYYCDGLIKIRLCHNEAALKDFRAFLENLTMVLEQATCQSALSTFGEIDAFLISVNDHKQIYIK +HFMMDEKKTNIDEKMEMAVHQPLVSLLLREQQRNEHQLHLRAQIYGRTEQFAQRQSVEAPYHTCIGIVNTCLFLLVNAGL +QKWLFADGRNLQWALILHLTSLGLGSLVAARMRIPLLTYAIYVFFVPCWLGASPSRPDAALAGGVQVAALIGLVVYSVVW +MSDQRFSHRNCVVMLGVFLAAACALLAVYAPQPRAPAAHFALLVATLLVLVAMLLTLSSQNMQFFYRQYLRELKASRFQK +SQFVQVLRRWCSRGSRPVADPAVEATGGATTTVETDEFGLAVARLGLEKGKGPGGRRIFADDQWPCRPPGAPTPSPPEAD +RLCSMYRPTCFGGARTGRRRSRKQGNREGWATKREDVKPVLLGSFWSM +>DECOY_114 +PLDSKDTGEAQAGPETGSPSLLTRRNYHGKIIGTNNNENLLQKQRQRNLSQVLGLVVAALSYQGPLRRPPLIFPNPQVRG +LLFYTKIKGEQESIGKVYIEGRYDFAFGQDKLILYTEEPVQIRGSVGTSDMRSALNVTKGWIDYQPKKAGIVGAVVSGHS +IGIRLEFNNFSHKNIEQISETLALSFDALACLHGWKDECQQKEPSLGSVAMYTSGITKIKEIDQFRDEGLLEDFDAIIEN +LLRLCEVGQNNMETQSYFDAFGPISAFMVGVADYSQSYLEENDRDKELFHRAVHSPLINRLMNENHERLEKMENIEEKAQ +VRWLFDLRATYELQQGHYFVALLFMAMLLLSVEKTGLFDEGSHNLNDYRLFLGAYVTETLLAYIAIMILLVALKLVSNLR +LFVACTVMALVGTFVFYEPYSCIDTFVASSNFTLNKLPISKDFDCWLINLIAGLFNILISAFIIVNRALYTENIWCCTKR +LILPLCKYDEATTILVLASHLMILISFQITMPMVRSSPLLSQIATIFLLVIFACVLNSKFVEDRMQSYKHELSSDKFMLS +FPKIHERRLKDGSRLDITHEIRKNIEEPGSQVHLAQALHNPLLNISNRTLAALTNQKGVINDFPLEPSWSGETFTAGSNR +RDSSSVSEKVIDEPLSLLSDEPQKILYTEINHKRLFENREKGHGEEVNYDGNLCDLTAKSIHIRGPIGGSELKNAIDVDW +SWVDFQWKRLGLVGCLVSGSHIGIRMDVDHKTRSRVYRITKIMSLGMEVCCHAHDQRPEPLGSVCYYCDGLIKIRLCHHE +HALRDFRAFLENLMRVLEQASLTTSLNTFGKVDAFLISVNEYRHIYIRHFQHQLHEDEVNTMDNIMELVVFRPLVSLVLR +EQRQNETELRLRAEVCRRTELFAQRQARDSLYSIFIGATNMCMFLVAQAVVQNISIVALRPIVVQLIVQLLSTGLGALIA +WTLPLPLMSYTAFLTFLVYGIGDGLLGYGLGAALIQTTMAVWTVVGSYQLYTHSTTDKRVVVLACIVVEIGTFFGLLIGK +LPDMPASALSLHLVLLTLKTLVDLVNMVVESKRRQGLFYRQYLRELDRSKFSNRLTPFIVGRYSYGGNLFFDSNSPACDL +HLFGLDGGGGSGSASGSGSREPFVKTGCTSHAREGPGLSYLPLASDGSLQPAHHNPGGGAPDSAKGSGGSGSGSGGRHGH +IFRQETIHRVATQWLLRQPRSASRGDGAPPTPHITYLEESGTLCRVDSLEM +>DECOY_143 +GQSYHLVRHLPSVTSIPQLGLLQKTASDWDNGLELRPCISPYQGETRRVWESAQKIAEFAWPINRSISADDMKMLSKFVI +GEKELRTRIFQLVLMTAILDLLCERGKVGLSQIGKQKLFSHLGNTNLNLILGLEPTLKWFGDETQLSLLETWPVADQWHQ +ICVIEDEEKVELFCLISDDKTDCKIQLFCSDQLVESLEDSETDSSQFAFVPCRSGELSGVSEELLCLDVPTTRSQSCLAE +PLASAMPLRLNATLSAASPQFHFPSSASPHYSGFGRIPDPDTPLSFHLQPSDLEPFTGASPRTTFGGPHQLPASQASSLS +SGSFVIGCYPSSPPNQPPGTPCSASQPIWDACTGPVPGQSFQSADFQRPPAASGFSAVQRYSAFSLSAPSHARATPPLYS +GVAPALIPFFSSTSTEWPSVKKFLPETATPKCSETWSLDLLKEVGGRELNSTFAPLVGLGDEEFDESVEPQSLEMKRKSF +PIKRHKRKSLRLEPWESSALLSQNRVAEQPEGQWSMYPLFDVDEKAILESVKPIDPFPSENEDRKEVAVFSTFQTILSNE +KSLKIILSKLTQKKMEHSTENEHLIGDEYDRILARAALKHIMTGTTKQLETTSVMTRFEKEQILACLTAQTCHPIFGYVL +LRDNLFLSPVQAPAQLAEPVDPNLQQWKVSVSHCSPSCLRTMQDEIQKRWSHKSKANFYEFVGAGCQSLIRLVHRNATSG +IGCAFLRTHPRSRKVLQLTLSEDQLHGDSVLLINRSGRAPYLLSLYRLTKWFDTNGMTPTASMIFEAAMTNSTIHKPYSF +LEKYGTGFQIINVKQKEGVLSLAHLAIQKAQLFTVGEMSSSCDLCIIVESESALDPLDVDLDPQFVLMCAESEKEPHKEV +WMRPLYAASLGIHLSFGSSDLSSGEMTSIVAKCDTRKQKLEHTDSFIFEIVYPMEISMTLSFSQKTGIEKICIKEVTDQL +NENLAKDQQWPAVTAPMFFVGVTGLISLETIYTIKILVKAKPPLNGVSVTFVDPADQSMLYAGHGQTVAELYEQQAEEKE +KIEGVIHKGNIFAEFGCVAAKDDLPFIYKAEIPVHSKNTYTQFVIVQAVTDIIRGKIHVDELPVLNGSADQLGAKTSSST +KADPLQYDEVKSFNSFEPRYEELETHDSPHFDKIQDGPMSFKIIYKMKVQNTKYVVFEDDEFDTTVSATQSVGHVSDYGP +PAETLSFDKEHLDMCKGLAVDCILLLRTGDTEGPHSYKISTSLSDSFYIGSGLNGVDTRQVGRDEVVKPLLLGRCLIGVI +NQVPSGHLLPRVNGLKSLFETTENVRGVRFIQLVDVPSKSHHNQLVEKRVRLFEETNQEVHEIKCRLARYKALSPPNPKS +LNTECVNVMDRILQCLDAKKALLGLNVEKPMTGKHPILRYFETMMKQLQEATEGNKLAAKVLLLIGEAKSVDNLSIRNVP +KLLMHELHGLAEAWIMEVLDSVEQSLTSSNMVEELLLAQLQESALQTAEPTFHERLLFGQKKLEEIYNEFYESADESTKK +IAFQRRTEMGDDLLFHSSILFPCDRSDRSCQLEVVVAEQGGEMGVKELTNYKAVEFDQPLHPIEVNQMGFETLEVTDEEE +TASDPCLGETKVESSSAKQDPPPTIDLPKYPDYNKVDLLRKERISKWIFDPNAIHVHNKQISNLQYQSLVDANDLIIHTC +QPNLSFSFKGGNEKIDTQLKKKQQQPLYKVKLCFICNAFIGMVM +>DECOY_213 +LGLAAQSAAVLKKGEEAFCTEKDDAKCCKEVFAAFDDMVAKLQEKTAKPKHKVLEVLATQKKIQREKESLTCIDAHFTFT +EANFEKPVYTEDVELASFCPRRNVLSETCCKTVRDSVPTKEHLVCLQNLVVSLYDEACPMRKAEPHKCCKSGVKGLNRSV +EVLTPTSVQPVKKTYRVLLANQFKYEGLQEFLECNQKILNQPEEVLPKFEDFVKAYCEHPDAAACCKELTTEYTKALRLL +LVVSYDPHRRAYEYLFMGLFVDKAEAYNKCVDKSEVFDAALSPLDAPMEDNEVEAICHSKELLPKECCEKLKSSISDQNE +CIYKALDARDDACELLDGHCCETHVKTLDTVLKSVEAFEAKPFRQSLRAVAWAKFAREGFKQLSACKLRQKASSAKGEDR +LEDLKPLLCAAKDAAQCCETFAAKYRKAFFLLEPAYFYPHRRAIEYLYKKLFTEENDHFATCMVDVEPRVLRPLNPNDDK +HQLFCENREPEQKACCDAMEGYTERLTAVTCLKDGFLTHLSKDCNEASEDAVCTKAFETVENVLKVHDEFPCQQLYQAFA +ILVLAKFNEEGLDKFRHAVESKHADRRFVGRSYASSFLFLLSIFTVWKM +>DECOY_230 +YAHNAIYLSQAAAGGDEGSGEYKGQAALGNVEARKIFEETAAGANDRQGRWANLASAQLARGYSFTLAWPRPLPCRNIAN +LNFSAEEESQGGSLFTVGPVAPPVTRRLATVTAMAIEEPTYKIPCAHGPTVMNPKLLTGELYVHHDSLAKYVAALVKETV +YQCRKLDHDGDPLIEPEVIPVIGNQQCISAYRALVNANELIALASPTRESIKLVCRWKAFDAGDKKYQACRESLGDLGQT +TTEGDTGALPVVGKDVKIGVVIGKDQITRVFPVGNDDKQYLTEHFFIVGGICKKVRDDASFLVQRYLRRNEETNEVGIQS +LRKAMSGVSEDAALIGKGPAVIRLAIDSLEKKQEASLAPYSHPM +>DECOY_231 +FEEHFPYDKHSTCSLLACVRWNRNYSLLTTMDQSSLEFDFVKFNEAIREPTVSKPIVVLNRQMPFRILVQATTKNHKAAI +AKIRPDELLSPDEPKAWPRDPSGLPSYATVVIGKSQCYQILKEQTLYPHCEIQNVAPKYKLGPKNLIMEVQLHNFNSIGI +AKVLGEDVLEEMAAWTDLINTDSPVVNGSEDLPFFEKGPKFGTPWHILYLDLYDLKLDSLTKQCAGKVLGKEHYTCWLKS +VIFLEERKVVQERLKEQIAVGVENENQYVHACDIHRYGVDIAVKVAETVQGPPSKWTGLGLIPMKAGNNLLLRSAM +>DECOY_242 +ISISNEILVPDLYYYPIPLCKNRQRIDHSIQNLRQRFAEISRRPAEEVFHIDPFHGLPRRDDPERSLTWLVLLTICTTKV +DPLTDMFTELTTLGKTQIPPNRMSAPFNPMWATFEMQGTNVAAHKASCTYIVITVYRILEPVTRLCRPFGSSERGLLCEK +FIEQVWSQLEPDGEVAADSPYYYTIIETVYKELANWVALSDDRYYYGPLDQVGREVFDNPLYLSDYTLESLARVMVGAFG +EVGLSMGKASLGGENLLVARGISNIQVTYRTHPILLKYLPHCMPLNRLLALCFAEAILHTELLHAIAEHSYFEAYRVWTK +ALLWDWESDSPLFIPCDPGPTQSLQIAIPMMKGEPGFHLLCLPACHHQKRGSLEVTPIGEMIRYDALYINGKELEAQLCT +GEGLFPAVMDDTVPFKDPIRTCRRILGPNVGNLYQYGFFTDEAWHEAVYESVVSKKGPFIKRIDKLRKWSHKCDLLGRVK +FALAMPGLRVFFSATKLFSYRLNLNLFKTAKFNILIPFGPIYGNWEPRNPNRHRRVPPRYSPIHVYSPLGPLFVRWHYFD +QKARIEEKRHELLVPLSDDATTKGTAERLALTEYGDMWQYAPFHYIRGNPACIQVYNCYWPDKPFFAYREKHLRIIILEG +LDQPCQVTYQGVAGTAFDRGFHNLLQKHSEGQTGVITLSISDRTGSLLDTGTAVRVKYTAM
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool.conf Wed Mar 01 13:01:11 2017 -0500 @@ -0,0 +1,162 @@ +<?xml version='1.0' encoding='UTF-8'?> +<toolbox> + <section id="section-id-Peptidepropertyprediction" name="Peptide property prediction"> + <tool file="openms/PTModel.xml"/> + <tool file="openms/PTPredict.xml"/> + <tool file="openms/RTModel.xml"/> + <tool file="openms/RTPredict.xml"/> + </section> + <section id="section-id-DEFAULT" name="DEFAULT"> + <tool file="openms/OpenSwathFileSplitter.xml"/> + <tool file="openms/OpenSwathMzMLFileCacher.xml"/> + </section> + <section id="section-id-TargetedExperiments" name="Targeted Experiments"> + <tool file="openms/ConvertTraMLToTSV.xml"/> + <tool file="openms/ConvertTSVToTraML.xml"/> + <tool file="openms/InclusionExclusionListCreator.xml"/> + <tool file="openms/MRMMapper.xml"/> + <tool file="openms/OpenSwathAnalyzer.xml"/> + <tool file="openms/OpenSwathAssayGenerator.xml"/> + <tool file="openms/OpenSwathChromatogramExtractor.xml"/> + <tool file="openms/OpenSwathConfidenceScoring.xml"/> + <tool file="openms/OpenSwathDecoyGenerator.xml"/> + <tool file="openms/OpenSwathDIAPreScoring.xml"/> + <tool file="openms/OpenSwathFeatureXMLToTSV.xml"/> + <tool file="openms/OpenSwathRewriteToFeatureXML.xml"/> + <tool file="openms/OpenSwathRTNormalizer.xml"/> + <tool file="openms/PrecursorIonSelector.xml"/> + </section> + <section id="section-id-Utilities" name="Utilities"> + <tool file="openms/AccurateMassSearch.xml"/> + <tool file="openms/CVInspector.xml"/> + <tool file="openms/DecoyDatabase.xml"/> + <tool file="openms/DeMeanderize.xml"/> + <tool file="openms/Digestor.xml"/> + <tool file="openms/DigestorMotif.xml"/> + <tool file="openms/ERPairFinder.xml"/> + <tool file="openms/FFEval.xml"/> + <tool file="openms/FuzzyDiff.xml"/> + <tool file="openms/IDDecoyProbability.xml"/> + <tool file="openms/IDExtractor.xml"/> + <tool file="openms/IDMassAccuracy.xml"/> + <tool file="openms/IDScoreSwitcher.xml"/> + <tool file="openms/IDSplitter.xml"/> + <tool file="openms/LabeledEval.xml"/> + <tool file="openms/LowMemPeakPickerHiRes.xml"/> + <tool file="openms/LowMemPeakPickerHiRes_RandomAccess.xml"/> + <tool file="openms/MapAlignmentEvaluation.xml"/> + <tool file="openms/MassCalculator.xml"/> + <tool file="openms/MetaboliteSpectralMatcher.xml"/> + <tool file="openms/MetaProSIP.xml"/> + <tool file="openms/MRMPairFinder.xml"/> + <tool file="openms/MRMTransitionGroupPicker.xml"/> + <tool file="openms/MSSimulator.xml"/> + <tool file="openms/MultiplexResolver.xml"/> + <tool file="openms/MzMLSplitter.xml"/> + <tool file="openms/OpenSwathWorkflow.xml"/> + <tool file="openms/QCCalculator.xml"/> + <tool file="openms/QCEmbedder.xml"/> + <tool file="openms/QCExporter.xml"/> + <tool file="openms/QCExtractor.xml"/> + <tool file="openms/QCImporter.xml"/> + <tool file="openms/QCMerger.xml"/> + <tool file="openms/QCShrinker.xml"/> + <tool file="openms/RNPxl.xml"/> + <tool file="openms/RNPxlXICFilter.xml"/> + <tool file="openms/RTEvaluation.xml"/> + <tool file="openms/SemanticValidator.xml"/> + <tool file="openms/SequenceCoverageCalculator.xml"/> + <tool file="openms/SimpleSearchEngine.xml"/> + <tool file="openms/SpecLibCreator.xml"/> + <tool file="openms/SvmTheoreticalSpectrumGeneratorTrainer.xml"/> + <tool file="openms/TICCalculator.xml"/> + <tool file="openms/TopPerc.xml"/> + <tool file="openms/TransformationEvaluation.xml"/> + <tool file="openms/XMLValidator.xml"/> + </section> + <section id="section-id-MapAlignment" name="Map Alignment"> + <tool file="openms/ConsensusMapNormalizer.xml"/> + <tool file="openms/FeatureLinkerLabeled.xml"/> + <tool file="openms/FeatureLinkerUnlabeled.xml"/> + <tool file="openms/FeatureLinkerUnlabeledQT.xml"/> + <tool file="openms/MapRTTransformer.xml"/> + </section> + <section id="section-id-IDProcessing" name="ID Processing"> + <tool file="openms/ConsensusID.xml"/> + <tool file="openms/FalseDiscoveryRate.xml"/> + <tool file="openms/FidoAdapter.xml"/> + <tool file="openms/IDConflictResolver.xml"/> + <tool file="openms/IDFileConverter.xml"/> + <tool file="openms/IDFilter.xml"/> + <tool file="openms/IDMapper.xml"/> + <tool file="openms/IDPosteriorErrorProbability.xml"/> + <tool file="openms/IDRTCalibration.xml"/> + <tool file="openms/LuciphorAdapter.xml"/> + <tool file="openms/PeptideIndexer.xml"/> + <tool file="openms/PhosphoScoring.xml"/> + </section> + <section id="section-id-Signalprocessingandpreprocessing" name="Signal processing and preprocessing"> + <tool file="openms/BaselineFilter.xml"/> + <tool file="openms/ExternalCalibration.xml"/> + <tool file="openms/HighResPrecursorMassCorrector.xml"/> + <tool file="openms/InternalCalibration.xml"/> + <tool file="openms/MapNormalizer.xml"/> + <tool file="openms/MassTraceExtractor.xml"/> + <tool file="openms/NoiseFilterGaussian.xml"/> + <tool file="openms/NoiseFilterSGolay.xml"/> + <tool file="openms/PeakPickerHiRes.xml"/> + <tool file="openms/PeakPickerIterative.xml"/> + <tool file="openms/PeakPickerWavelet.xml"/> + <tool file="openms/PrecursorMassCorrector.xml"/> + <tool file="openms/SpectraMerger.xml"/> + <tool file="openms/TOFCalibration.xml"/> + </section> + <section id="section-id-Identification" name="Identification"> + <tool file="openms/CompNovoCID.xml"/> + <tool file="openms/CompNovo.xml"/> + <tool file="openms/InspectAdapter.xml"/> + <tool file="openms/MascotAdapter.xml"/> + <tool file="openms/MascotAdapterOnline.xml"/> + <tool file="openms/MSGFPlusAdapter.xml"/> + <tool file="openms/ProteinInference.xml"/> + <tool file="openms/SpectraFilterBernNorm.xml"/> + <tool file="openms/SpectraFilterMarkerMower.xml"/> + <tool file="openms/SpectraFilterNLargest.xml"/> + <tool file="openms/SpectraFilterNormalizer.xml"/> + <tool file="openms/SpectraFilterParentPeakMower.xml"/> + <tool file="openms/SpectraFilterScaler.xml"/> + <tool file="openms/SpectraFilterSqrtMower.xml"/> + <tool file="openms/SpectraFilterThresholdMower.xml"/> + <tool file="openms/SpectraFilterWindowMower.xml"/> + <tool file="openms/XTandemAdapter.xml"/> + </section> + <section id="section-id-FileHandling" name="File Handling"> + <tool file="openms/DTAExtractor.xml"/> + <tool file="openms/FileConverter.xml"/> + <tool file="openms/FileFilter.xml"/> + <tool file="openms/FileInfo.xml"/> + <tool file="openms/FileMerger.xml"/> + <tool file="openms/IDMerger.xml"/> + <tool file="openms/IDRipper.xml"/> + <tool file="openms/MapStatistics.xml"/> + <tool file="openms/MzTabExporter.xml"/> + <tool file="openms/TextExporter.xml"/> + </section> + <section id="section-id-Quantitation" name="Quantitation"> + <tool file="openms/AdditiveSeries.xml"/> + <tool file="openms/Decharger.xml"/> + <tool file="openms/EICExtractor.xml"/> + <tool file="openms/FeatureFinderCentroided.xml"/> + <tool file="openms/FeatureFinderIdentification.xml"/> + <tool file="openms/FeatureFinderIsotopeWavelet.xml"/> + <tool file="openms/FeatureFinderMetabo.xml"/> + <tool file="openms/FeatureFinderMRM.xml"/> + <tool file="openms/FeatureFinderMultiplex.xml"/> + <tool file="openms/FeatureFinderSuperHirn.xml"/> + <tool file="openms/IsobaricAnalyzer.xml"/> + <tool file="openms/ITRAQAnalyzer.xml"/> + <tool file="openms/ProteinQuantifier.xml"/> + <tool file="openms/ProteinResolver.xml"/> + <tool file="openms/TMTAnalyzer.xml"/> + </section> +</toolbox>